2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.javascript.json.JSON;
25 import java.awt.Component;
26 import java.awt.Dimension;
27 import java.awt.Toolkit;
28 import java.awt.event.MouseEvent;
29 import java.io.BufferedReader;
31 import java.io.FileOutputStream;
32 import java.io.FileReader;
33 import java.io.IOException;
34 import java.io.InputStream;
35 import java.io.InputStreamReader;
36 import java.io.Reader;
38 import java.util.Properties;
40 import javax.swing.SwingUtilities;
42 import org.json.simple.parser.JSONParser;
43 import org.json.simple.parser.ParseException;
45 import java.util.HashMap;
46 import java.util.HashSet;
48 import java.util.logging.ConsoleHandler;
49 import java.util.logging.Level;
50 import java.util.logging.Logger;
51 import com.stevesoft.pat.Regex;
53 import swingjs.api.JSUtilI;
56 * System platform information used by Applet and Application
63 private static boolean isJS = /** @j2sNative true || */
66 private static JSUtilI jsutil = /**
67 * @j2sNative new Clazz.new_("swingjs.JSUtil")
73 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
76 private static Boolean isHeadless = null;
79 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
83 public static boolean isMac()
86 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
91 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
95 public static boolean isWin()
98 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
104 * @return true if HTML5 JavaScript
106 public static boolean isJS()
112 * sorry folks - Macs really are different
114 * BH: disabled for SwingJS -- will need to check key-press issues
116 * @return true if we do things in a special way.
118 public static boolean isAMacAndNotJS()
120 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
124 * Check if we are on a Microsoft plaform...
126 * @return true if we have to cope with another platform variation
128 public static boolean isWindowsAndNotJS()
130 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
135 * @return true if we are running in non-interactive no UI mode
137 public static boolean isHeadless()
139 if (isHeadless == null)
141 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
148 * @return nominal maximum command line length for this platform
150 public static int getMaxCommandLineLength()
152 // TODO: determine nominal limits for most platforms.
153 return 2046; // this is the max length for a windows NT system.
157 * Answers the input with every backslash replaced with a double backslash (an
158 * 'escaped' single backslash)
163 public static String escapeBackslashes(String s)
165 return s == null ? null : s.replace("\\", "\\\\");
169 * Answers true if the mouse event has Meta-down (Command key on Mac) or
170 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
171 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
172 * Mac, you can use e.isPopupTrigger().
177 public static boolean isControlDown(MouseEvent e)
179 return isControlDown(e, isMac());
183 * Overloaded version of method (to allow unit testing)
189 protected static boolean isControlDown(MouseEvent e, boolean aMac)
193 return e.isControlDown();
195 // answer false for right mouse button
196 // shortcut key will be META for a Mac
197 return !e.isPopupTrigger()
198 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
199 & e.getModifiers()) != 0;
200 // could we use e.isMetaDown() here?
203 // BH: I don't know about that previous method. Here is what SwingJS uses.
204 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
206 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
207 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
209 // if (id != MouseEvent.MOUSE_RELEASED)
212 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
213 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
215 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
217 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
221 // // mac, linux, unix
222 // if (id != MouseEvent.MOUSE_PRESSED)
224 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
225 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
226 // return rt || (ctrl && lt);
232 * Windows (not Mac, Linux, or Unix) and right button to test for the
233 * right-mouse pressed event in Windows that would have opened a menu or a
239 public static boolean isWinRightButton(MouseEvent e)
241 // was !isAMac(), but that is true also for Linux and Unix and JS,
243 return isWin() && SwingUtilities.isRightMouseButton(e);
247 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
248 * without pressing the button.
253 public static boolean isWinMiddleButton(MouseEvent e)
255 // was !isAMac(), but that is true also for Linux and Unix and JS
256 return isWin() && SwingUtilities.isMiddleMouseButton(e);
259 public static boolean allowMnemonics()
264 public final static int TIME_RESET = 0;
266 public final static int TIME_MARK = 1;
268 public static final int TIME_SET = 2;
270 public static final int TIME_GET = 3;
272 public static long time, mark, set, duration;
277 * Platform.timeCheck(null, Platform.TIME_MARK);
281 * Platform.timeCheck("some message", Platform.TIME_MARK);
283 * reset...[set/mark]n...get
288 public static void timeCheck(String msg, int mode)
290 long t = System.currentTimeMillis();
298 System.err.println("Platform: timer reset\t\t\t" + msg);
304 // total time between set/mark points
305 duration += (t - set);
315 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
316 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
327 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
328 + "\t" + ((duration) / 1000f) + "\t" + msg);
335 ////// jsutil additions, simplifications
337 public static void cacheFileData(String path, Object data)
341 jsutil.cachePathData(path, data);
345 public static void cacheFileData(File file)
349 byte[] bytes = getFileBytes(file);
352 cacheFileData(file.toString(), bytes);
357 public static byte[] getFileBytes(File f)
359 return (isJS() && f != null ? jsutil.getBytes(f) : null);
362 public static byte[] getFileAsBytes(String fileStr)
364 byte[] bytes = (isJS() && fileStr != null
365 ? (byte[]) jsutil.getFile(fileStr, false)
369 cacheFileData(fileStr, bytes);
374 public static String getFileAsString(String url)
379 ret = (String) jsutil.getFile(url, true);
382 cacheFileData(url, ret);
388 public static boolean setFileBytes(File f, String urlstring)
394 byte[] bytes = getFileAsBytes(urlstring);
398 jsutil.setFileBytes(f, bytes);
399 } catch (Throwable t)
401 System.out.println("Platform.setFileBytes failed: " + t);
406 public static void addJ2SBinaryType(String ext)
410 jsutil.addBinaryFileType(ext);
415 * Encode the URI using JavaScript encodeURIComponent
418 * @return encoded value
420 public static String encodeURI(String value)
423 * @j2sNative value = encodeURIComponent(value);
429 * Open the URL using a simple window call if this is JavaScript
432 * @return true if window has been opened
434 public static boolean openURL(String url) throws IOException
438 BrowserLauncher.openURL(url);
450 public static String getUniqueAppletID()
452 // Caution -- null here means using current thread instead of a known component.
454 return jsutil.getAppletForComponent(null)._getID();
458 * Read the Info block for this applet.
463 * @return unique id for this applet
465 public static void readInfoProperties(String prefix, Properties p)
469 jsutil.readInfoProperties(prefix, p);
473 public static void setAjaxJSON(URL url)
481 public static Object parseJSON(InputStream response)
482 throws IOException, ParseException
486 return JSON.parse(response);
489 BufferedReader br = null;
492 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
493 return new JSONParser().parse(br);
501 } catch (IOException e)
509 public static Object parseJSON(String json) throws ParseException
511 return (isJS() ? JSON.parse(json)
512 : new JSONParser().parse(json));
515 public static Object parseJSON(Reader r)
516 throws IOException, ParseException
525 return new JSONParser().parse(r);
527 // Using a file reader is not currently supported in SwingJS JavaScript
529 if (r instanceof FileReader)
531 throw new IOException(
532 "StringJS does not support FileReader parsing for JSON -- but it could...");
534 return JSON.parse(r);
539 * Dump the input stream to an output file.
543 * @throws IOException
544 * if the file cannot be created or there is a problem reading the
547 public static void streamToFile(InputStream is, File outFile)
550 if (isJS() && jsutil.streamToFile(is, outFile))
554 FileOutputStream fio = new FileOutputStream(outFile);
557 byte[] bb = new byte[32 * 1024];
559 while ((l = is.read(bb)) > 0)
570 * Add a known domain that implements access-control-allow-origin:*
572 * These should be reviewed periodically.
575 * for a service that is not allowing ajax
577 * @author hansonr@stolaf.edu
580 public static void addJ2SDirectDatabaseCall(String domain)
585 jsutil.addDirectDatabaseCall(domain);
590 * Retrieve the first query field as command arguments to Jalview. Include
591 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
592 * element to this value.
595 @SuppressWarnings("unused")
596 public static void getURLCommandArguments()
602 String[] args = null;
605 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
606 * + "?").split("?")[1].split("#")[0]); args && (args =
611 jsutil.setAppletInfo("args", args);
618 * A (case sensitive) file path comparator that ignores the difference between /
626 public static boolean pathEquals(String path1, String path2)
630 return path2 == null;
636 String p1 = path1.replace('\\', '/');
637 String p2 = path2.replace('\\', '/');
638 return p1.equals(p2);
641 ///// new methods from applet branch only
644 public static URL getDocumentBase()
646 return (isJS() ? jsutil.getDocumentBase() : null);
649 public static URL getCodeBase()
651 return (isJS() ? jsutil.getCodeBase() : null);
654 public static void ensureJmol()
658 jsutil.loadResourceIfClassUnknown("core/core_jvjmol.z.js",
659 "org.jmol.viewer.Viewer");
663 public static void ensureRegex()
667 jsutil.loadResourceIfClassUnknown("core/core_stevesoft.z.js",
668 "com.stevesoft.pat.Regex");
672 public static Regex newRegex(String searchString, String replaceString)
675 return (replaceString == null ? new Regex(searchString)
676 : new Regex(searchString, replaceString));
679 public static Regex newRegexPerl(String code)
682 return Regex.perlCode(code);
686 * Initialize Java debug logging. A representative sample -- adapt as desired.
688 public static void startJavaLogging()
694 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
695 "java.awt.Component", "java.awt.focus.Component",
696 "java.awt.event.Component",
697 "java.awt.focus.DefaultKeyboardFocusManager");
702 * Initiate Java logging for a given class. Only for Java, not JavaScript;
703 * Allows debugging of complex event processing.
707 public static void logClass(String... classNames)
715 Logger rootLogger = Logger.getLogger("");
716 rootLogger.setLevel(Level.ALL);
717 ConsoleHandler consoleHandler = new ConsoleHandler();
718 consoleHandler.setLevel(Level.ALL);
719 for (int i = classNames.length; --i >= 0;)
721 Logger logger = Logger.getLogger(classNames[i]);
722 logger.setLevel(Level.ALL);
723 logger.addHandler(consoleHandler);
729 * Set the "app" property of the HTML5 applet object, for example,
730 * "testApplet.app", to point to the Jalview instance. This will be the object
731 * that page developers use that is similar to the original Java applet object
732 * that was accessed via LiveConnect.
736 public static void setAppClass(Object app)
740 jsutil.setAppletAttribute("app", app);
745 * Retrieve the object's embedded size from a div's style on a page if
746 * embedded in SwingJS.
749 * JFrame or JInternalFrame
750 * @param defaultWidth
751 * use -1 to return null (no default size)
752 * @param defaultHeight
753 * @return the embedded dimensions or null (no default size or not embedded)
755 public static Dimension getDimIfEmbedded(Component frame,
756 int defaultWidth, int defaultHeight)
758 Dimension d = (Dimension) getEmbeddedAttribute(frame, "dim");
759 return (d == null && defaultWidth >= 0
760 ? new Dimension(defaultWidth, defaultHeight)
766 * If this frame Is this frame embedded in a web page, return a known type.
769 * a JFrame or JInternalFrame
771 * @return null if frame is not embedded.
773 public static Object getEmbeddedAttribute(Component frame, String type)
775 return (isJS() ? jsutil.getEmbeddedAttribute(frame, type) : null);
779 * Only called for JavaScript.
781 * @return Map for static singleton classes unique to a given applet
783 public static HashMap<?, ?> getJSSingletons()
785 return (isJS() ? jsutil.getJSContext("jssingletons") : null);
789 * By designating initialCapacity and loadFactor, we tell SwingJS to use a
790 * standard (slower) Java HashMap to back this HashSet, thus providing exactly
791 * the same iterator order (until a new Java version changes it!)
793 * @return a standard Java HashSet
795 public static Set<String> getJavaOrderedHashSet()
797 return new HashSet<>(16, 0.75f);
801 * Switch the flag in SwingJS to use or not use the JavaScript Map object in
802 * any Hashtable, HashMap, or HashSet. Default is enabled.
804 * For testing purposes only.
807 public static boolean setJavaScriptMapObjectEnabled(boolean enabled)
813 jsutil.setJavaScriptMapObjectEnabled(enabled);
814 HashSet<String> hs = new HashSet<>();
815 // Java hash table iterator in HashMap will return "one" before "two"
816 // because of its hash code;
817 // JavaScript Map object will return "two" first because it was added first.
820 return (hs.iterator().next() == (enabled ? "two" : "one"));
824 public static void stackTrace()
826 new NullPointerException("testing only").printStackTrace();
831 * escape a string according to the local platform's escape character
834 * @return escaped file
836 public static String escapeString(String file)
838 StringBuffer f = new StringBuffer();
839 int p = 0, lastp = 0;
840 while ((p = file.indexOf('\\', lastp)) > -1)
842 f.append(file.subSequence(lastp, p));
846 f.append(file.substring(lastp));